Visualizing RNA-Seq reads aligned onto a genome

This image from IGB shows short read sequences aligned onto the Arabidopsis A_thaliana_Jun_2009 (TAIR9) genome. The track above the Coordinates track presents part of two Arabidopsis gene models, with sequence data loaded. Note how the reads seem to support two alternative splicing variations in the overlapping gene. Also note the nucleotide differences between the aligned reads (upper track) and the reference sequence.